ENT MERFISH Report
1. Overview
1.1 Sample Information
A brief sample information is generated from the submission table for the following analysis.
| Expt | Sample | Index | Case_Number | Sex | Age | HPV | Sample_Region | Genotype | Group | Region | DataPath | Clinic.comment |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | NT28530x2 | NT28530 | 1 | M | 52 | Negative | Left posterior BOT | NT | Normal | region_NT28530x2 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
| 1 | TT28519x1 | TT28519 | 1 | M | 52 | Negative | Left posterior BOT | TT | Tumor | region_TT28519x1 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
| 1 | TT28519x2 | TT28519_dup | 1 | M | 52 | Negative | Left posterior BOT | TT | Tumor | region_TT28519x2 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
| 1 | NT28530x1 | NT28530_dup | 1 | M | 52 | Negative | Left posterior BOT | NT | Normal | region_NT28530x1 | Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 | Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K. |
1.2 MERSCOPE Data Quality Summary
The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.
Generally, log10 transcript count > 4.0 in most area can be considered as a good quality standard for human tissue.
Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.
1.2.1 NT28530x2(Normal)
1.2.2 TT28519x1(Tumor)
1.2.3 TT28519x2(Tumor)
1.2.4 NT28530x1(Normal)
1.3 Transcript Mis-Match on FOV Boundary
Due to issues with the Vizgen software, transcript alignment is incorrect during decoding, leading to misalignment problems at the field of view (FOV) boundary.
Vizgen has solved this issue by temporarily updating the decoding software to an unpublished beta version.
However, this update also made the “vzg” file being upgraded to “vzg2”. Current Vizgen Visualizer cannot recognize the new data format, which made Visualizer unusable for this dataset.
1.4 Autofluorescent issue
Autofluorescence is a major problem limiting the sensitivity of the detection of the fluorescence specifically derived from the applied dye or probe. As we can find it on DAPI imaging, there are many over-bright region.
Autofluorescence may occur due to the incomplete clearance of the tissue. Because of the presence of autofluorescence, the decoding would be confounded and the results in these cells would be artifacts.
As Dr. Tan highly recommends, we removed the portion of cell with autofluorescent issue, for better accuracy.
NT28530_DAPI_Imaging
NT28530_DAPI_Imaging_small
NT28530_dup_DAPI_Imaging
NT28530_dup_DAPI_Imaging_small
2. Data Processing & Analysis
2.1 Cell Segmentation & Filtering
Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.
To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 2000], and the gene count per cell > 25.
After that, we successfully obtained high-quality and accurate cell and gene data. We are now ready to perform statistical analysis.
For analysis platform, all of the analysis and visualization are performed using Scanpy, a commonly used Python package toolkit for analyzing single-cell gene expression data.
2.1.2 Transcript Count Violin
The transcript level is a basic aspect of data quality control. After filtering, we have ensured that the minimum transcript count per cell > 25.
Transcript Count Violin After Filtering
2.2 Batch Effect & Dimension Reduction
We conducted Leiden UMAP clustering, a non-linear, manifold-aware dimension reduction algorithm, on our dataset to subset the cells into clusters. The following annotations are based on the umap clustering.
Umap of cells and colored by batch
3.Cell Annotation
To annotate individual cell types, we found the marker genes from database CellMarker.
We utilize FCRL5 and MZB1 for the identification of B cells, CCND1 and NOTCH1 for cancer cells, CD83 for dendritic cells, PLVAP and PDK4 for endothelial cells, and COL1A1 for fibroblasts. For macrophages, we apply CD14 in conjunction with CD163, while KIT is employed for mast cells, and TRAC, GATA3, and CD5 are used for T cells.
It is good to note that, so far what we have is a preliminary annotation, and we can potentially achieve further resolution on some cell types. For instance, T cells can be subdivided into regulatory T cells, helper T cells, natural killer T cells, and so on. However, the current sample size is insufficient for these detailed classifications. Once we have enough samples, further annotation should be feasible.
3.1 Markers for type annotation
3.2 Cell Type Umap
3.3 Cell Type Spatial Map
With the annotations, we can map cell types back to their physical positions and create a spatial map for each sample.
3.4 Cancer & T cell & B cell Spatial Map
3.5 Cell Type Qualification Analysis
| cell_type_2 | NT28530 | NT28530_dup | TT28519 | TT28519_dup | Total |
|---|---|---|---|---|---|
| B cell | 2 | 3 | 1230 | 1031 | 2266 |
| Cancer cell | 34 | 30 | 465 | 362 | 891 |
| Dendritic | 2 | 0 | 133 | 110 | 245 |
| Endothelial | 1609 | 1427 | 1722 | 1341 | 6099 |
| Fibroblast | 2059 | 1732 | 19739 | 18582 | 42112 |
| Macrophage | 308 | 270 | 1915 | 1732 | 4225 |
| Mast cell | 35 | 33 | 474 | 486 | 1028 |
| Smooth muscle cell | 374 | 285 | 1644 | 1367 | 3670 |
| T cell | 115 | 82 | 811 | 676 | 1684 |
| Total | 4538 | 3862 | 28133 | 25687 | 62220 |
3.6 Cell Type Proportion Analysis
Based on the quantification of individual cell types, we are capable to compare the differences in cell numbers between various samples and genotypes. The proportion of each cell type is calculated by dividing the count of that specific cell type by the total cell count. The results are then visualized in a bar plot.
Notably, B cells, mast cells, and T cells show an obvious increase in tumor samples.
4. Gene differentiation
Here, we use Wilcoxon rank-sum test to compute gene differential expression (DE). P value are adjusted using Benjamini–Hochberg procedure. The statistical significance was cut-off by log2(Fold Change) > 2 or log2(Fold Change) < -2 and p_value < 0.05.
The result are visualized via Volcano plot: a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change).
The comparison is between Tumor and Normal samples. A positive fold change means higher expression in the tumor group.
4.1 all
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| COL1A1 | 128.719830 | 85.216440 | 0.0000000 | 0.0000000 |
| FN1 | 81.286490 | 7.571341 | 0.0000000 | 0.0000000 |
| FOS | -46.969980 | -6.759444 | 0.0000000 | 0.0000000 |
| PDK4 | -60.815765 | -6.633553 | 0.0000000 | 0.0000000 |
| COL5A1 | 80.329340 | 6.229767 | 0.0000000 | 0.0000000 |
| EGR1 | -34.539925 | -5.055663 | 0.0000000 | 0.0000000 |
| VEGFA | -39.941800 | -5.038070 | 0.0000000 | 0.0000000 |
| CD79A | 5.999517 | 4.959108 | 0.0000000 | 0.0000000 |
| JUN | -66.503334 | -4.828621 | 0.0000000 | 0.0000000 |
| GPX3 | -34.578636 | -3.987802 | 0.0000000 | 0.0000000 |
| MZB1 | 6.797644 | 3.979829 | 0.0000000 | 0.0000000 |
| SERPINA1 | 11.236790 | 3.931262 | 0.0000000 | 0.0000000 |
| FCRL5 | 4.486988 | 3.772412 | 0.0000072 | 0.0000276 |
| CX3CL1 | -8.829576 | -3.658773 | 0.0000000 | 0.0000000 |
| POU2AF1 | 17.934225 | 3.616645 | 0.0000000 | 0.0000000 |
| FAP | 6.151611 | 3.492644 | 0.0000000 | 0.0000000 |
| TNC | 32.630886 | 3.387915 | 0.0000000 | 0.0000000 |
| DES | -31.869339 | -3.284775 | 0.0000000 | 0.0000000 |
| TNF | 9.065383 | 3.131130 | 0.0000000 | 0.0000000 |
| MYH11 | -5.373700 | -3.080815 | 0.0000001 | 0.0000004 |
| DUSP1 | -52.305590 | -3.073642 | 0.0000000 | 0.0000000 |
| XBP1 | 6.826031 | 3.048380 | 0.0000000 | 0.0000000 |
| MMP9 | 11.337405 | 3.016693 | 0.0000000 | 0.0000000 |
| RORC | -14.309868 | -2.970993 | 0.0000000 | 0.0000000 |
| MMP11 | 14.401033 | 2.840110 | 0.0000000 | 0.0000000 |
| BMP1 | 54.718426 | 2.823937 | 0.0000000 | 0.0000000 |
| COL11A1 | 25.157415 | 2.791966 | 0.0000000 | 0.0000000 |
| CCR2 | 5.268528 | 2.779894 | 0.0000001 | 0.0000006 |
| CR2 | 4.689729 | 2.658455 | 0.0000027 | 0.0000109 |
| TP63 | -4.827339 | -2.616780 | 0.0000014 | 0.0000057 |
| CXCL1 | 6.437659 | 2.539849 | 0.0000000 | 0.0000000 |
| PPARGC1A | -4.273971 | -2.511725 | 0.0000192 | 0.0000717 |
| JUNB | -35.787884 | -2.490444 | 0.0000000 | 0.0000000 |
| DERL3 | 3.310865 | 2.451468 | 0.0009301 | 0.0028356 |
| ITGAX | 5.390393 | 2.434840 | 0.0000001 | 0.0000003 |
| LGR6 | -2.549464 | -2.431690 | 0.0107889 | 0.0275226 |
| LGR5 | -5.406462 | -2.327275 | 0.0000001 | 0.0000003 |
| MUC1 | 9.941775 | 2.272612 | 0.0000000 | 0.0000000 |
| HGF | 4.867999 | 2.261392 | 0.0000011 | 0.0000047 |
| CD19 | 2.838978 | 2.259758 | 0.0045258 | 0.0125717 |
| IRF4 | 3.012619 | 2.251352 | 0.0025900 | 0.0075292 |
| FLI1 | 5.158706 | 2.239080 | 0.0000002 | 0.0000011 |
| NCAM1 | -16.123442 | -2.227492 | 0.0000000 | 0.0000000 |
| CLCA1 | 3.899802 | 2.198663 | 0.0000963 | 0.0003366 |
| PIK3CG | 6.211835 | 2.155691 | 0.0000000 | 0.0000000 |
| CD248 | 30.015327 | 2.120976 | 0.0000000 | 0.0000000 |
| ESCO2 | 2.790225 | 2.114788 | 0.0052671 | 0.0143129 |
| TNFRSF13C | 2.781648 | 2.100781 | 0.0054084 | 0.0145386 |
| CD27 | 2.849136 | 2.088706 | 0.0043838 | 0.0122453 |
| LOX | 4.607403 | 2.082753 | 0.0000041 | 0.0000161 |
| CHEK2 | 7.125153 | 2.082282 | 0.0000000 | 0.0000000 |
| TNFRSF9 | 3.862387 | 2.075009 | 0.0001123 | 0.0003845 |
| SPRY2 | -21.701843 | -2.025791 | 0.0000000 | 0.0000000 |
| SH2D1B | -3.089103 | -2.014404 | 0.0020076 | 0.0058702 |
| IL6R | -19.968603 | -2.006788 | 0.0000000 | 0.0000000 |
4.2 Cancer cell
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| FOS | -9.674765 | -18.332428 | 0.0000000 | 0.0000000 |
| COL1A1 | 10.273704 | 15.094367 | 0.0000000 | 0.0000000 |
| ATF3 | -6.680579 | -7.325389 | 0.0000000 | 0.0000000 |
| JUNB | -6.519753 | -6.353756 | 0.0000000 | 0.0000000 |
| EGR1 | -6.436063 | -4.904849 | 0.0000000 | 0.0000000 |
| JUN | -6.486479 | -4.801098 | 0.0000000 | 0.0000000 |
| DUSP1 | -5.359185 | -4.615851 | 0.0000001 | 0.0000052 |
| FLT4 | 3.672781 | 4.157596 | 0.0002399 | 0.0074977 |
| COL5A1 | 3.294915 | 3.599521 | 0.0009845 | 0.0259082 |
| LMNA | -3.604216 | -3.569431 | 0.0003131 | 0.0092087 |
| FN1 | 4.274744 | 3.321740 | 0.0000191 | 0.0007973 |
| COL4A1 | 5.705288 | 3.206742 | 0.0000000 | 0.0000008 |
| THBD | -4.691177 | -2.850006 | 0.0000027 | 0.0001235 |
| PROX1 | 3.904441 | 2.778789 | 0.0000944 | 0.0036324 |
| MYC | -4.748903 | -2.713153 | 0.0000020 | 0.0001023 |
| EPHB4 | 5.087696 | 2.504998 | 0.0000004 | 0.0000201 |
| ETS1 | 3.751177 | 2.027703 | 0.0001760 | 0.0058669 |
| PKM | 3.832851 | 2.000154 | 0.0001267 | 0.0045238 |
4.3 Dendritic
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| NA | NA | NA | NA | NA |
| :—–: | :——: | :————–: | :—–: | :———: |
4.4 Endothelial
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| VEGFA | -35.816616 | -10.077840 | 0.0000000 | 0.0000000 |
| COL1A1 | 47.572320 | 9.932630 | 0.0000000 | 0.0000000 |
| PLVAP | 38.004112 | 9.664353 | 0.0000000 | 0.0000000 |
| PDK4 | -34.856445 | -7.034097 | 0.0000000 | 0.0000000 |
| COL4A1 | 35.776917 | 5.580956 | 0.0000000 | 0.0000000 |
| PECAM1 | 27.437399 | 4.532059 | 0.0000000 | 0.0000000 |
| SERPINE1 | 20.581670 | 4.145850 | 0.0000000 | 0.0000000 |
| COL5A1 | 16.131900 | 4.142918 | 0.0000000 | 0.0000000 |
| MMP11 | 3.607988 | 3.250464 | 0.0003086 | 0.0016072 |
| KIT | 3.419221 | 3.240729 | 0.0006280 | 0.0030785 |
| RORC | -14.886651 | -3.145059 | 0.0000000 | 0.0000000 |
| CXCL2 | -4.145788 | -3.131462 | 0.0000339 | 0.0002016 |
| LMNA | 28.933674 | 3.093195 | 0.0000000 | 0.0000000 |
| ACTA2 | 10.422846 | 3.086447 | 0.0000000 | 0.0000000 |
| PDGFRB | 11.492411 | 2.996124 | 0.0000000 | 0.0000000 |
| CD248 | 5.186810 | 2.958897 | 0.0000002 | 0.0000015 |
| NEDD4 | -14.398186 | -2.812049 | 0.0000000 | 0.0000000 |
| IL6R | -14.629830 | -2.766724 | 0.0000000 | 0.0000000 |
| MMRN1 | 6.903936 | 2.753270 | 0.0000000 | 0.0000000 |
| CD276 | 8.340302 | 2.740798 | 0.0000000 | 0.0000000 |
| PPARGC1A | -4.913524 | -2.547583 | 0.0000009 | 0.0000060 |
| TGFBR2 | 23.386492 | 2.544253 | 0.0000000 | 0.0000000 |
| FN1 | 21.659600 | 2.516487 | 0.0000000 | 0.0000000 |
| TGFB1 | 14.458306 | 2.510600 | 0.0000000 | 0.0000000 |
| SH2D1B | -3.437823 | -2.446839 | 0.0005864 | 0.0029030 |
| ENG | 20.407070 | 2.388739 | 0.0000000 | 0.0000000 |
| ETS1 | 20.198217 | 2.334731 | 0.0000000 | 0.0000000 |
| CTSW | 4.125513 | 2.294079 | 0.0000370 | 0.0002126 |
| CLEC14A | 20.905638 | 2.275434 | 0.0000000 | 0.0000000 |
| TP63 | -4.689392 | -2.272294 | 0.0000027 | 0.0000176 |
| E2F1 | 3.179068 | 2.174574 | 0.0014775 | 0.0067775 |
| WWTR1 | 19.532927 | 2.166429 | 0.0000000 | 0.0000000 |
| VWF | 20.648241 | 2.120249 | 0.0000000 | 0.0000000 |
| ITGA5 | 19.046722 | 2.072308 | 0.0000000 | 0.0000000 |
| SELP | 8.094025 | 2.045839 | 0.0000000 | 0.0000000 |
| CD40 | 11.831773 | 2.011925 | 0.0000000 | 0.0000000 |
4.5 Fibroblast
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| COL1A1 | 99.661520 | 109.207320 | 0.0000000 | 0.0000000 |
| FOS | -47.059372 | -10.880125 | 0.0000000 | 0.0000000 |
| EGR1 | -50.041943 | -10.419629 | 0.0000000 | 0.0000000 |
| FN1 | 58.055080 | 8.389499 | 0.0000000 | 0.0000000 |
| JUN | -63.418068 | -7.511326 | 0.0000000 | 0.0000000 |
| COL5A1 | 58.653736 | 6.514852 | 0.0000000 | 0.0000000 |
| PDK4 | -36.407936 | -6.081756 | 0.0000000 | 0.0000000 |
| GPX3 | -34.492940 | -5.962629 | 0.0000000 | 0.0000000 |
| SERPINA1 | 9.758843 | 4.440912 | 0.0000000 | 0.0000000 |
| CCR2 | 4.496484 | 3.799526 | 0.0000069 | 0.0000326 |
| RET | -3.050877 | -3.763918 | 0.0022817 | 0.0082672 |
| TNC | 28.061033 | 3.746374 | 0.0000000 | 0.0000000 |
| DUSP1 | -42.866486 | -3.717051 | 0.0000000 | 0.0000000 |
| FLI1 | 4.938783 | 3.521752 | 0.0000008 | 0.0000040 |
| SPRY2 | -28.405836 | -3.440419 | 0.0000000 | 0.0000000 |
| BCL2 | -21.041565 | -3.361053 | 0.0000000 | 0.0000000 |
| IL6R | -11.209660 | -3.353977 | 0.0000000 | 0.0000000 |
| TNF | 6.995335 | 3.302661 | 0.0000000 | 0.0000000 |
| FAP | 5.171738 | 3.295502 | 0.0000002 | 0.0000012 |
| HLA-DPA1 | 2.532061 | 3.215192 | 0.0113394 | 0.0363443 |
| KLF2 | -22.494427 | -3.147081 | 0.0000000 | 0.0000000 |
| PREX2 | -9.170182 | -3.143904 | 0.0000000 | 0.0000000 |
| TGFBI | 14.967690 | 3.113704 | 0.0000000 | 0.0000000 |
| PLA2G2A | -10.403379 | -2.908959 | 0.0000000 | 0.0000000 |
| CR2 | 4.180466 | 2.905692 | 0.0000291 | 0.0001359 |
| BMP1 | 42.859085 | 2.858506 | 0.0000000 | 0.0000000 |
| EPHA2 | -5.979615 | -2.842888 | 0.0000000 | 0.0000000 |
| EGFR | -36.323550 | -2.792461 | 0.0000000 | 0.0000000 |
| TEAD4 | 4.601498 | 2.774775 | 0.0000042 | 0.0000202 |
| LGR5 | -5.319131 | -2.760852 | 0.0000001 | 0.0000006 |
| MMP11 | 10.715138 | 2.731303 | 0.0000000 | 0.0000000 |
| PGF | -6.036967 | -2.727679 | 0.0000000 | 0.0000000 |
| SOD2 | -21.268118 | -2.698692 | 0.0000000 | 0.0000000 |
| NFKBIA | -37.298576 | -2.643214 | 0.0000000 | 0.0000000 |
| CXCL1 | 5.260466 | 2.607160 | 0.0000001 | 0.0000008 |
| S100A9 | -3.774349 | -2.586396 | 0.0001604 | 0.0006741 |
| HGF | 3.872809 | 2.472608 | 0.0001076 | 0.0004678 |
| CLCA1 | 3.283746 | 2.400243 | 0.0010244 | 0.0040014 |
| FZD7 | -21.664896 | -2.394277 | 0.0000000 | 0.0000000 |
| JUNB | -20.558294 | -2.368409 | 0.0000000 | 0.0000000 |
| CDK6 | 12.404665 | 2.341559 | 0.0000000 | 0.0000000 |
| POU2AF1 | 10.431594 | 2.292325 | 0.0000000 | 0.0000000 |
| CD1C | 2.798475 | 2.265068 | 0.0051344 | 0.0171148 |
| CXCL2 | 7.335484 | 2.252299 | 0.0000000 | 0.0000000 |
| COL11A1 | 19.515144 | 2.240313 | 0.0000000 | 0.0000000 |
| MET | -2.514364 | -2.211613 | 0.0119247 | 0.0379769 |
| MMP9 | 8.479343 | 2.173744 | 0.0000000 | 0.0000000 |
| ZAP70 | 7.108235 | 2.166870 | 0.0000000 | 0.0000000 |
| COL4A1 | -14.409939 | -2.116672 | 0.0000000 | 0.0000000 |
| MUC1 | 8.429799 | 2.110764 | 0.0000000 | 0.0000000 |
| PDGFRA | -24.080532 | -2.103632 | 0.0000000 | 0.0000000 |
| LOX | 3.660348 | 2.065853 | 0.0002519 | 0.0010239 |
| LGALS9 | 2.994693 | 2.004917 | 0.0027472 | 0.0097419 |
| IL1R2 | -3.184731 | -2.000739 | 0.0014489 | 0.0054882 |
4.6 Macrophage
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| COL1A1 | 29.665201 | 21.313148 | 0.0000000 | 0.0000000 |
| FOS | -22.637910 | -12.442084 | 0.0000000 | 0.0000000 |
| MMP9 | 5.213645 | 6.499431 | 0.0000002 | 0.0000044 |
| SPP1 | 4.578217 | 6.127543 | 0.0000047 | 0.0000977 |
| FN1 | 17.229155 | 5.819446 | 0.0000000 | 0.0000000 |
| EGR1 | -17.853518 | -4.971041 | 0.0000000 | 0.0000000 |
| TREM2 | 5.923193 | 4.002033 | 0.0000000 | 0.0000001 |
| PDK4 | -14.654759 | -3.942336 | 0.0000000 | 0.0000000 |
| MRC1 | -16.989233 | -3.646870 | 0.0000000 | 0.0000000 |
| ITGAX | 13.298241 | 3.640879 | 0.0000000 | 0.0000000 |
| COL5A1 | 10.114567 | 3.443203 | 0.0000000 | 0.0000000 |
| DUSP1 | -13.914675 | -2.867081 | 0.0000000 | 0.0000000 |
| THBD | -8.767480 | -2.502315 | 0.0000000 | 0.0000000 |
| CD248 | 3.794988 | 2.477330 | 0.0001477 | 0.0018006 |
| PKM | 11.442293 | 2.380384 | 0.0000000 | 0.0000000 |
| HIF1A | 5.919156 | 2.233082 | 0.0000000 | 0.0000001 |
| LRP1 | 12.007602 | 2.061832 | 0.0000000 | 0.0000000 |
4.7 Mast cell
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| COL1A1 | 11.554090 | 30.175860 | 0.0000000 | 0.0000000 |
| FN1 | 3.923991 | 4.566871 | 0.0000871 | 0.0075897 |
| VEGFA | -6.816688 | -4.331221 | 0.0000000 | 0.0000000 |
| COL5A1 | 3.746050 | 4.181580 | 0.0001796 | 0.0128315 |
| SFRP2 | 3.621788 | 4.016486 | 0.0002926 | 0.0182859 |
| NFKB2 | -6.765123 | -3.871854 | 0.0000000 | 0.0000000 |
| ICAM1 | -4.836095 | -2.638979 | 0.0000013 | 0.0001655 |
| CSF1 | 3.913213 | 2.463667 | 0.0000911 | 0.0075897 |
4.8 Smooth Muscle cell
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| COL1A1 | 36.033295 | 35.535330 | 0.0000000 | 0.0000000 |
| COL4A1 | 27.172250 | 7.101044 | 0.0000000 | 0.0000000 |
| FOS | -14.032536 | -6.647189 | 0.0000000 | 0.0000000 |
| JUN | -15.592484 | -5.803882 | 0.0000000 | 0.0000000 |
| FN1 | 18.829844 | 5.127449 | 0.0000000 | 0.0000000 |
| TNF | 4.487255 | 4.998678 | 0.0000072 | 0.0000863 |
| COL5A1 | 21.033014 | 4.751438 | 0.0000000 | 0.0000000 |
| ACTA2 | -14.657331 | -4.576652 | 0.0000000 | 0.0000000 |
| JUNB | -17.292665 | -4.422530 | 0.0000000 | 0.0000000 |
| LGR6 | -5.308680 | -4.066671 | 0.0000001 | 0.0000017 |
| MYH11 | -15.415986 | -4.019932 | 0.0000000 | 0.0000000 |
| PDGFRB | 11.228720 | 3.559115 | 0.0000000 | 0.0000000 |
| CHEK2 | 2.926007 | 3.364132 | 0.0034334 | 0.0264110 |
| PDK4 | -9.583596 | -3.270993 | 0.0000000 | 0.0000000 |
| PTGDR2 | -2.747317 | -3.097388 | 0.0060085 | 0.0406734 |
| DUSP1 | -14.434421 | -3.063678 | 0.0000000 | 0.0000000 |
| SERPINE1 | 9.548772 | 3.017724 | 0.0000000 | 0.0000000 |
| E2F1 | 3.277156 | 2.942244 | 0.0010486 | 0.0095326 |
| ATF3 | -11.208811 | -2.790443 | 0.0000000 | 0.0000000 |
| PLVAP | 6.595327 | 2.787905 | 0.0000000 | 0.0000000 |
| MMP11 | 7.006973 | 2.598386 | 0.0000000 | 0.0000000 |
| BMP1 | 14.924097 | 2.452774 | 0.0000000 | 0.0000000 |
| CX3CL1 | -3.627839 | -2.451389 | 0.0002858 | 0.0029164 |
| CD248 | 13.306128 | 2.423763 | 0.0000000 | 0.0000000 |
| ICAM3 | 4.481207 | 2.389812 | 0.0000074 | 0.0000863 |
| DES | -6.431553 | -2.373101 | 0.0000000 | 0.0000000 |
| SFRP2 | 5.309166 | 2.353069 | 0.0000001 | 0.0000017 |
| MYBL2 | 2.944799 | 2.263086 | 0.0032316 | 0.0256479 |
| CD276 | 6.821728 | 2.071905 | 0.0000000 | 0.0000000 |
4.9 T cell
| names | scores | logfoldchanges | pvals | pvals_adj |
|---|---|---|---|---|
| COL1A1 | 18.528063 | 34.526530 | 0.0000000 | 0.0000000 |
| FN1 | 8.459756 | 5.744955 | 0.0000000 | 0.0000000 |
| CD40LG | -5.212253 | -2.767354 | 0.0000002 | 0.0000311 |
| FOS | -3.901277 | -2.126768 | 0.0000957 | 0.0053159 |
| COL5A1 | 4.896749 | 2.073000 | 0.0000010 | 0.0000974 |
| CTSW | 3.538528 | 2.022379 | 0.0004024 | 0.0167652 |
5. Supplements
For original pictures and more details, please use the google drive link: ENT MERFISH Supplement